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Related Experiment Video

Updated: Jan 25, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Modulating RNA secondary and tertiary structures by mismatch binding ligands.

Asako Murata¹, Masayuki Nakamori², Kazuhiko Nakatani¹

¹Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.

Methods (San Diego, Calif.)

|May 13, 2019

Summary

Researchers developed novel small molecules, mismatch binding ligands (MBLs), designed to target non-canonical RNA structures. These MBLs offer potential for developing drugs against diseases linked to non-coding RNA.

Keywords:

Huntington disease Mismatch binding ligands Molecular glue Myotonic dystrophy Programmed ribosomal frameshift Surface plasmon resonance

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Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

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Published on: December 12, 2017

Area of Science:

Medicinal Chemistry
Molecular Biology
Drug Discovery

Background:

Over 75% of the human genome is transcribed into RNA, with non-coding RNAs playing crucial roles in cellular processes and disease.
Non-coding RNAs present significant opportunities for pharmaceutical research, particularly for targeting undruggable and rare diseases.
Small organic molecules binding to non-canonical nucleic acid structures, especially RNA, are gaining attention.

Purpose of the Study:

To describe the hypothesis and outcomes of designing small molecules, mismatch binding ligands (MBLs), for targeting non-canonical DNA and RNA structures.
To review the development of MBLs based on in silico design principles targeting mismatched base pairs in nucleic acids.
To highlight the success in developing MBLs that bind to biologically significant DNA and RNA motifs, with a focus on RNA targeting.

Main Methods:

In silico design of synthetic molecules (MBLs) based on hydrogen-bonding and semi-intercalation hypotheses.
MBLs designed with two heterocycles to bind mismatched nucleotide bases via hydrogen bonding, forming pseudo-base pairs.
Evaluation of MBLs' binding capabilities to non-canonical DNA and RNA structures.

Main Results:

Several MBLs have been successfully developed that bind to specific DNA and RNA motifs.
The design hypothesis, while not universally applicable to all mismatched base pairs, has yielded effective ligands.
Demonstrated success in creating MBLs with potential for targeting RNA structures.

Conclusions:

The developed MBLs show promise as therapeutic agents targeting non-canonical RNA structures.
This approach offers a pathway for developing novel drugs against diseases associated with non-coding RNA dysregulation.
Further research into MBLs could unlock new treatments for challenging and rare diseases.